Every once in a while, I push down permissions to /Applications and /Library myself, just to make sure that everything is root/admin read-write / read-write / read. Then, I repair permissions afterward, just to be safe. This way any third party files I've installed in these two places have the permissions I want.
However, doing so causes a slowdown. You will get the spinning rainbow cursor when any system-wide authentication window, even the login window, prompts you for your password. This is very bad, as if you are someone like me, get this authentication prompt about 10 times a day, on average.
After much frustration, I searched Google. I couldn't find anything. I search a second and third time, a few months later, nothing. I finally decided to search once more, and found an answer! I wanted to post it here, so it's easier to find the answer for anyone else who may be searching.
René's fix was to change the owner of specific files, but I find it much easier to delete the /Library/Caches folder and reboot. It's too bad repair permissions can't fix these cache files as well. I know this happens on 10.4 and 10.3, but I'm not sure about 10.2.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050811215315810